Sourdough Chocolate Chip Bagels (Same-Day or Overnight)
This post may contain affiliate links. Please read our disclosure policy.
This Sourdough Chocolate Chip Bagels recipe takes my well-loved Sourdough Bagels and gives them a chocolatey upgrade. They have the same chewy texture and simple process you already love, but with pockets of melty chocolate chips tucked into every bite.
You can bake them the same day or let the dough rest overnight for fresh bagels in the morning, whichever fits your schedule best. And if you need something a little faster, you can use my Sourdough Discard Bagels recipe and follow the exact same process for delicious homemade chocolate chip bagels in less time.
Quick Look: Sourdough Chocolate Chip Bagels
- Prep Time: 10 minutes
- Rise Time: 10 hours
- Bake Time: 20 minutes
- Total Time: 10 hours 30 minutes
- Servings: 8 bagels
- Calories: ~334 kcal per bagel
- Cook Method: Boiled, then baked
- Flavor Profile: Soft and chewy with a lightly firm crust and melty pockets of chocolate throughout. Intermediate — Simple ingredients and mostly hands-off with an overnight rise, plus a quick boiling step before baking.
SUMMARIZE & SAVE THIS CONTENT ON
Why You’ll Love This Sourdough Chocolate Chip Bagels Recipe
- Perfectly Chewy Texture with a Thin, Firm Crust: Boiling the bagels in a large pot of water with honey before baking creates that classic chewy texture and golden brown crust. The result is homemade sourdough bagels that are soft inside and lightly firm on the outside similar to my Sourdough Bagels and Sourdough Blueberry Bagels.
- Flexible Same-Day or Overnight Schedule: This sourdough bagel recipe works around your plans. Mix the dough in the morning and bake by dinner, or let it rest overnight in the fridge for a second rise and boil them fresh the next day. I use this same flexible approach with my Sourdough Cinnamon Raisin Bagels.
- Loaded with Chocolate Chips: Semi-sweet chocolate chips (or dark chocolate, chocolate chunks, or even cocoa powder-dusted white chocolate) fold into the dough and soften in the oven without losing their shape. Every bite has melty, gooey pockets of chocolate that complement the mild sourdough tang just like in my Sourdough Chocolate Chip Cookies.
Ingredients & Substitutions
* To find precise measurements, scroll to the bottom of this post to find the recipe card*
- Sourdough Starter – An active and bubbly starter will give you the best rise for these chewy sourdough chocolate bagels. If you’re looking for something faster, check out my sourdough discard bagel recipe that’s ready to bake in just 2 hours. Instead of an active sourdough starter, I used discard, and I must say there was a slight difference in flavor.
- Bread Flour – You can use all-purpose flour for these homemade bagels, but bread flour is recommended for its higher protein content. Plus, the bagels come out with a chewier texture.
- Chocolate Chips – I used semi-sweet chocolate chips, but you can use your favorite chocolate like dark chocolate, milk chocolate, or white chocolate chips. For smaller pops of chocolate, use mini chocolate chips. There are plenty of options for you, chocolate lovers!
- Sugar – I used white sugar for a touch of sweetness, but you can use alternatives like cane sugar or honey.
- Honey – Adding a little bit of honey to the boil bath gives your chocolate chip sourdough bagels the perfect golden brown, chewy crust once they are baked. Honey can be substituted with brown sugar or maple syrup as well.
Baking Schedule #1
|
Time |
Process |
|---|---|
|
8:00 AM |
Mix dough |
|
8:30 AM |
Knead dough |
|
8:30 AM |
First dough rise |
|
4:30 PM |
Shaping and Second rise |
|
5:30 PM |
Boil and bake |
Baking Schedule #2
|
Time |
Process |
|---|---|
|
DAY 1 |
|
|
10:00 PM |
Mix dough |
|
10:30 PM |
Knead dough |
|
10:30 PM |
First rise |
|
DAY 2 |
|
|
6:30 AM |
Shaping and Second Rise |
|
7:30 AM |
Boil and bake |
How to Make Sourdough Chocolate Chip Bagels
- To the bowl of your stand mixer, add the sourdough starter, water and sugar. Mix until smooth.
- To the wet ingredients, add the dry ingredients, flour and salt. Mix again on low speed until everything is incorporated, then knead the dough with a dough hook on medium speed for about 5-6minutes, until the dough is smooth, pulls away from the sides of the bowl, and feels tacky to the touch.
- Remove the dough and place it in a lightly greased bowl. Cover and let the bagel dough rise for 30 minutes.
- After 30 minutes, pour the chocolate chips on top of the dough and knead for 20 seconds or until a smooth dough ball forms. Use a stretch-and-fold motion, pulling the dough up and folding it toward the center, pressing down with your palm. Cover again and wait until it doubles in size.
- Once the sourdough bagel dough has doubled in size, punch it down to remove all of the air bubbles. Then, place the dough on a lightly floured work surface.
- Using a bench scraper, divide the dough into 8 equal pieces, about 130 grams each.
- Pull the corners of each piece toward the center, flip, and then roll each piece of dough into a tight, round dough ball. Chocolate chips may pop out and this is normal. Use your thumb to punch a hole in the middle of the dough ball. Stretch the dough ball with both thumbs to about 2 inches wide, then place each bagel on a parchment-lined baking sheet. Repeat with the remaining pieces of dough.
- Cover the baking sheet with this plastic cover and let the dough rest for its second rise.
- The final proof is complete when the bagels have grown and look puffy. At 70°F, this usually takes 1–2 hours, or 3–4 hours if the dough is cold from the fridge.
- Prepare the boil bath. Bring a large pot of water to a boil, add honey, and stir until dissolved. Boil 2–3 bagels at a time, 30 seconds on each side. Remove with a slotted spoon and place on a wire rack.
- Bake at 425°F for 20–25 minutes or until golden brown and the internal temperature reaches 200–210°F.
- Cool slightly before slicing. Enjoy!
McKenna’s Helpful Tips
- Use a bubbly, active starter for the best rise: Your active sourdough starter should be at its peak — doubled in size and full of bubbles — before you mix the dough. If you want a faster option using sourdough discard instead, try my Sourdough Discard Bagels which are ready in about 2 hours.
- Knead with a dough hook on medium speed: Use the bowl of your stand mixer fitted with a dough hook and knead on low to medium speed for 8-10 minutes until the dough is smooth and pulls away from the sides. If you don’t have a stand mixer, you can knead by hand on a lightly floured surface for about 12 minutes.
- Add chocolate chips after the first rise: Let the bagel dough rise for 30 minutes first, then fold in the chocolate chips. This prevents the chips from interfering with gluten development. For more tips on adding mix-ins to dough, check out my Sourdough Inclusions Guide.
- Don’t skip the honey boil bath: Boiling water with a bit of honey gives baked bagels their signature chewy crust and golden brown exterior. Boil 2-3 bagels at a time, 30 seconds per side, and remove with a slotted spoon to a wire rack. You can substitute maple syrup or brown sugar if needed.
- Try other chocolate variations: Swap semi-sweet chips for dark chocolate chunks, mini chocolate chips, or even a swirl of peanut butter on top before baking. If you love chocolate and sourdough together, also try my Chocolate Sourdough Focaccia with Peanut Butter or my Double Chocolate Espresso Sourdough Bread.
How to Store
These bagels are best enjoyed the day they’re baked, but you can definitely store them if needed. Store them in an airtight container at room temperature for up to 2 days. For longer storage, slice them and pop them in a zip-top bag in the freezer for up to a month. Toast or warm them in the oven to bring back that tender, chewy inside and lightly firm crust. If you refrigerate the dough overnight instead of baking right away, cover it well so it ferments slowly and is easy to shape in the morning.
Sourdough Chocolate Chip Bagels FAQs
Can I use sourdough discard instead of an active starter in this Sourdough Chocolate Chip Bagels Recipe?
Yes, sourdough discard works, but the flavor will be milder and the first rise will take longer. If you use discard, expect a longer dough rest for the bagels to develop structure. For a faster discard-based option, check out my Sourdough Discard Bagels which are ready to bake in just 2 hours.
Can I use all-purpose flour instead of bread flour for my Sourdough Chocolate Chip Bagels?
Yes, all-purpose flour will work, but bread flour gives the bagels more chew and helps them hold their shape better. Bread flour has a higher protein content, which creates that chewier texture that makes homemade bagels so satisfying. Using all-purpose may make them a bit softer, but they’ll still taste great.
Why do you boil the bagels before baking in your Sourdough Chocolate Chip Bagels Recipe?
Boiling in a large pot of water with honey gives the bagels their classic chewy texture and sets the crust. It helps them hold their shape in the oven and creates a thin, slightly firm exterior while keeping the inside soft and tender. The water may turn slightly brown as some chocolate melts. This is completely normal.
Can I make this Sourdough Chocolate Chip Bagels Recipe without chocolate chips?
Absolutely! You can leave them out entirely for plain sourdough bagels, or swap in other mix-ins like raisins, cinnamon sugar, or chocolate chunks. Without the chocolate chips, the bagels won’t have those soft, melty pockets, so the chew will feel a bit different. For a raisin version, try my Sourdough Cinnamon Raisin Bagels.
If you tried this Sourdough Chocolate Chip Bagels recipe or any other recipe on my blog, please leave a 🌟 star rating and let me know how it went in the📝 comments below. Thanks for visiting!
Sourdough Chocolate Chip Bagels Recipe
Yield: 8 bagels
These 100% Sourdough Chocolate Chip Bagels are just like my original sourdough bagels– soft, chewy interiors, lightly firm crusts, but now with melty chocolate pockets. Bake same day or overnight.
Want To Save This Recipe?
Enter your email below, and we’ll send it straight to your inbox! Plus, you’ll get my newest sourdough recipes and best tips every week!
Equipment
- Large Pot
Ingredients
Sourdough Whole Wheat Bagels
- 150 grams active sourdough starter 2/3 cup
- 250 grams water, warm 1 cup + 1 Tablespoon
- 500 grams bread flour 3 1/2 cups
- 40 grams sugar 3 Tablespoons
- 11 grams salt 1 1/2 teaspoons
- 100 grams chocolate chips 1/2 cup
Boil Bath
- 2400 grams water 10 cups
- 24 grams honey 1 Tablespoon
Instructions
Make Dough
- To the bowl of a stand mixer, add all of the bagel ingredients, except the chocolate chips, and mix again on low speed for 5-6 minutes. The dough should be smooth and tacky to the touch.My water was 110 degrees F. The water shouldn't be hotter than 120 degrees F – otherwise this can kill the sourdough starter. You can also mix and knead the dough by hand.150 grams active sourdough starter, 250 grams water, warm, 500 grams bread flour, 40 grams sugar, 11 grams salt
- Remove the dough and knead until smooth. Do so by folding a portion of the dough towards the center and pressing down with the heel of your hand. Repeat about 20 times, then place it in a lightly greased, straight-edged bowl. Cover and leave to rest for 30 minutes.
- After 30 minutes, of resting, pour the chocolate chips on top of the bagel dough. Knead the chocolate chips into the bagel dough by stretching a small piece of the dough up, folding it towards the middle, and pushing the dough down with the heel of your hand. Repeat this for about 30 seconds or until the chocolate chips are incorporated into the dough. Some of the chocolate chips won’t be fully mixed in, and that’s okay. We will correct this during shaping. Cover again and wait until the dough doubles in size.This took about 8-10 hours in my 70 degree F kitchen. The timing depends greatly on the temperature of your dough and environment. The warmer it is, the faster the dough will rise. The opposite is true for cooler kitchens.100 grams chocolate chips
- Once the dough has doubled in size, you can either cover the dough and store it in the fridge overnight, shape the bagels and store in the fridge overnight or proceed to shaping right away.Refer to the Notes before for Make-Ahead options.
- When ready to shape, punch it down to remove all of the air bubbles. Then, place the dough on a clean work surface. Using a bench scraper, divide the dough into 8 equal pieces, about 130 grams each.
- Pull the corners of each piece toward the center, pinch the seams together, flip, and then roll each piece of dough into a tight, round dough ball. Use your thumb to punch a hole in the middle of the dough ball. Some chocolate chips may escape, you can tuck them back in or leave them out. Stretch the dough ball with both thumbs about 2 inches, then place each bagel on a baking sheet lined with parchment paper. Repeat with the remaining pieces of dough.
- Cover the baking sheet with this plastic cover and let the dough rest for its second rise. The final proof is complete when the bagels have grown and look puffy.In my 70 degree F kitchen, this took about 1-2 hours with room temperature dough. If the dough is cold from being in the fridge, the second rise took more like 3-4 hours.
- Once the second rise is almost complete, prepare the boil bath. Fill a large pot with about 10 cups of water. Once the water is boiling, add the honey and stir until it is dissolved. Boil 2-3 bagels at a time, 30 seconds on each side. Use a slotted spoon to remove each bagel and place them on a wire rack. Repeat with the remaining bagels.You will notice that the water will turn brown due to some of chocolate chips melting. This is expected and won't effect the final product.24 grams honey, 2400 grams water
- Once all of the Sourdough Chocolate Chip Bagels have been boiled, place them on a parchment paper lined baking sheet. Preheat the oven to 425 degrees F.
- Bake the bagels for 20-25 minutes or until golden brown with an internal temperature of 205-210 degrees F.
- Cool slightly before slicing. Top with some butter or cream cheese and enjoy!
Notes
Refer to the sample baking schedule above.
Make-Ahead Options:
If you are looking to prepare these Sourdough Chocolate Chip Bagels the night before and bake them the following morning – here are some options and tips! Option 1: Prepare the dough and once it has doubled in size, cover the bowl and chill in the fridge overnight. The following morning, divide and shape the dough into bagels and allow them to rise and get fluffy in a warm place before baking as normal. Since the dough is cool from the fridge, the second rise will take longer to complete, about 3-4 hours in my 70 degree F kitchen. Option 2: Prepare the dough and shape the sourdough bagels the night before. Place them on a parchment-paper lined baking sheet and cover before placing them into the fridge overnight. Pull out the unbaked bagels to allow them to rise and get fluffy in a warm place. In my 70 degree F kitchen, this took about 2-4 hours.Ingredients & Substitutions
- Sourdough Starter – An active and bubbly starter will give you the best rise for these chewy bagels. If you’re looking for something faster, check out my sourdough discard bagel recipe that’s ready to bake in just 2 hours!
- Bread Flour – You technically can use all-purpose flour for these delicious bagels, but I highly suggest making it with bread flour, as it has a higher protein percentage. This allows the dough to rise at great lengths for a more chewy and enjoyable Sourdough Bagel.
- Sugar – I used white sugar for a touch of sweetness, but you can use alternate sugars like cane sugar or honey.
- Chocolate Chips – I used milk chocolate chips, but you can substitute them with any of your favorites like dark, white or even cinnamon chips!
Nutrition
Serving: 1g | Calories: 334kcal | Carbohydrates: 64g | Protein: 8g | Fat: 5g | Saturated Fat: 2g | Polyunsaturated Fat: 0.5g | Monounsaturated Fat: 0.1g | Sodium: 536mg | Potassium: 100mg | Fiber: 2g | Sugar: 15g | Vitamin A: 1IU | Vitamin C: 0.01mg | Calcium: 20mg | Iron: 1mg
Tried this recipe?Please leave a comment on the blog or share a photo on Instagram!
Sounds amazing but a question could I add coffee or espresso instead of water ?
I think that should work! Just keep in mind that coffee and espresso can slow down fermentation a bit, so your rise times may be a little longer than what’s listed in the recipe. I’d probably start by replacing just part of the water with coffee or espresso the first time and see how you like the flavor. It sounds like a delicious combination with the chocolate chips. If you give it a try, I would love to hear how it turns out!
I love your recipes and I love to make them. Thank you for posting them.
Thank you so much for the kind words! I’m so glad you’re enjoying the recipes and taking the time to make them—it truly means more than you know. Thanks for being here and baking along with me!
Perfectly delicious!!
So glad you enjoyed this recipe, Devin!
Love the little bits of chocolate in these chewy sourdough bagels. My family loves enjoying them straight out of the oven!